The occurrence of polyploidy, having multiple complete genomes, is now recognized as a major influence on the evolution, genetic composition, and diversification of many plant lineages. Polyploidy is widely viewed as following two pathways. An autopolyploid is one that is the result of genome doubling involving a single species. In contrast, an allopolyploid is a polyploid that is the result of hybridization between two or more species. Allopolyploidy can involve multiple independent hybridization events, which creates allopolyploid species that have several independently constructed genomes. The aquatic fern Salvinia molesta D.S. Mitch. belongs to a clade of closely related species known as the “Salvinia auriculata complex,” and is an allopentaploid hybrid with unknown parentage. Salvinia molesta is an invasive that can have devastating ecological effects on the freshwater ecosystems it colonizes. The lack of clarity surrounding the genomic composition of S. molesta complicates current eradication methods, as it is not clear how many genotypes are present and what these genotypes are. This research focuses on identifying the maternal genome of S. molesta and determining if this species consists of a single or multiple independently derived lineages. Whole chloroplast genome (plastome) sequencing from field-collected and herbarium specimens was used to establish the genetic diversity of S. molesta and the phylogenetic relationships among Salvinia species. The chloroplast phylogeny revealed that S. molesta and S. herzogii share the same plastome, although S. herzogii is unlikely to be S. molesta’s maternal parent due to its own status as a hybrid. Rather, we conclude that S. molesta’s maternal progenitor is either an undescribed, extant species or perhaps an extinct species. The observed plastome diversity within S. molesta indicates the presence of multiple divergent genotypes which strongly suggest multiple origins of this hybrid.